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Installation
Tutorials
Basics
Preprocessing and clustering
Preprocessing and clustering 3k PBMCs (legacy workflow)
Integrating data using ingest and BBKNN
Plotting
Core plotting functions
Customizing Scanpy plots
Trajectories
Trajectory inference for hematopoiesis in mouse
Experimental
How to preprocess UMI count data with analytic Pearson residuals
Using
dask
with Scanpy
Usage Principles
How to
Cell-Cycle Scoring and Regression
Using other kNN libraries in Scanpy
Plotting with Marsilea
API
Preprocessing:
pp
scanpy.pp.calculate_qc_metrics
scanpy.pp.filter_cells
scanpy.pp.filter_genes
scanpy.pp.highly_variable_genes
scanpy.pp.log1p
scanpy.pp.pca
scanpy.pp.normalize_total
scanpy.pp.regress_out
scanpy.pp.scale
scanpy.pp.sample
scanpy.pp.downsample_counts
scanpy.pp.recipe_zheng17
scanpy.pp.recipe_seurat
scanpy.pp.combat
scanpy.pp.harmony_integrate
scanpy.pp.scrublet
scanpy.pp.scrublet_simulate_doublets
scanpy.pp.hashsolo
scanpy.pp.bbknn
scanpy.pp.neighbors
Tools:
tl
scanpy.pp.pca
scanpy.tl.tsne
scanpy.tl.umap
scanpy.tl.draw_graph
scanpy.tl.diffmap
scanpy.tl.embedding_density
scanpy.tl.leiden
scanpy.tl.dendrogram
scanpy.tl.dpt
scanpy.tl.paga
scanpy.tl.ingest
scanpy.tl.rank_genes_groups
scanpy.tl.filter_rank_genes_groups
scanpy.tl.marker_gene_overlap
scanpy.tl.score_genes
scanpy.tl.score_genes_cell_cycle
Plotting:
pl
scanpy.pl.scatter
scanpy.pl.heatmap
scanpy.pl.dotplot
scanpy.pl.tracksplot
scanpy.pl.violin
scanpy.pl.stacked_violin
scanpy.pl.matrixplot
scanpy.pl.ranking
scanpy.pl.dot_area
scanpy.pl.clustermap
scanpy.pl.dendrogram
scanpy.pl.DotPlot
scanpy.pl.MatrixPlot
scanpy.pl.StackedViolin
scanpy.pl.highest_expr_genes
scanpy.pl.highly_variable_genes
scanpy.pl.scrublet_score_distribution
scanpy.pl.pca
scanpy.pl.ranking
scanpy.pl.pca_loadings
scanpy.pl.pca_variance_ratio
scanpy.pl.pca_overview
scanpy.pl.umap
scanpy.pl.tsne
scanpy.pl.diffmap
scanpy.pl.draw_graph
scanpy.pl.embedding_density
scanpy.pl.spatial
scanpy.pl.embedding
scanpy.pl.dpt_groups_pseudotime
scanpy.pl.dpt_timeseries
scanpy.pl.paga
scanpy.pl.paga_path
scanpy.pl.paga_compare
scanpy.pl.correlation_matrix
scanpy.pl.rank_genes_groups
scanpy.pl.rank_genes_groups_violin
scanpy.pl.rank_genes_groups_stacked_violin
scanpy.pl.rank_genes_groups_heatmap
scanpy.pl.rank_genes_groups_dotplot
scanpy.pl.rank_genes_groups_matrixplot
scanpy.pl.rank_genes_groups_tracksplot
Reading and Writing
scanpy.io.write
scanpy.io.read
scanpy.io.read_10x_h5
scanpy.io.read_10x_mtx
scanpy.io.read_h5ad
scanpy.io.read_csv
scanpy.io.read_excel
scanpy.io.read_hdf
scanpy.io.read_mtx
scanpy.io.read_text
scanpy.io.read_umi_tools
Get object from
AnnData
:
get
scanpy.get.obs_df
scanpy.get.var_df
scanpy.get.pca
scanpy.get.rank_genes_groups_df
scanpy.get.aggregate
Queries
scanpy.queries.biomart_annotations
scanpy.queries.mitochondrial_genes
scanpy.queries.enrich
Metrics
scanpy.metrics.modularity
scanpy.metrics.confusion_matrix
scanpy.metrics.gearys_c
scanpy.metrics.morans_i
Experimental
scanpy.experimental.pp.normalize_pearson_residuals
scanpy.experimental.pp.normalize_pearson_residuals_pca
scanpy.experimental.pp.highly_variable_genes
scanpy.experimental.pp.recipe_pearson_residuals
Classes
scanpy.Neighbors
Settings
scanpy.set_figure_params
scanpy.settings
scanpy.settings.override
scanpy.Preset
scanpy.Verbosity
scanpy.logging.print_header
Datasets
scanpy.datasets.blobs
scanpy.datasets.ebi_expression_atlas
scanpy.datasets.krumsiek11
scanpy.datasets.moignard15
scanpy.datasets.pbmc3k
scanpy.datasets.pbmc3k_processed
scanpy.datasets.pbmc68k_reduced
scanpy.datasets.paul15
scanpy.datasets.visium_sge
Deprecated functions
scanpy.pp.subsample
scanpy.pp.recipe_weinreb17
scanpy.tl.louvain
scanpy.tl.sim
scanpy.pl.sim
scanpy.queries.gene_coordinates
scanpy.datasets.toggleswitch
scanpy.logging.print_versions
scanpy.read_loom
scanpy.read_visium
External API
Preprocessing: PP
scanpy.external.pp.bbknn
scanpy.external.pp.mnn_correct
scanpy.external.pp.scanorama_integrate
scanpy.external.pp.hashsolo
scanpy.external.pp.magic
Tools: TL
scanpy.external.tl.phate
scanpy.external.tl.palantir
scanpy.external.tl.trimap
scanpy.external.tl.sam
scanpy.external.tl.phenograph
scanpy.external.tl.harmony_timeseries
scanpy.external.tl.wishbone
scanpy.external.tl.palantir
scanpy.external.tl.palantir_results
scanpy.external.tl.sandbag
scanpy.external.tl.cyclone
Plotting: PL
scanpy.external.pl.phate
scanpy.external.pl.trimap
scanpy.external.pl.sam
scanpy.external.pl.wishbone_marker_trajectory
Exporting
scanpy.external.exporting.spring_project
scanpy.external.exporting.cellbrowser
Release notes
Community
Contributing
Contributing code
Getting set up
Tests
Documentation
CI
Versioning
Making a release
Contributors
References
API
Plotting:
pl
scanpy.pl.StackedViolin
scanpy.pl.StackedViolin.DEFAULT_DENSITY_NORM
System Settings
Light
Dark
GitHub
Discourse
scverse.org
Core
AnnData
decoupler
MuData
Muon
Pertpy
rapids-singlecell
Scanpy
Scirpy
scvi-tools
SnapATAC2
SpatialData
Squidpy
Ecosystem
AESTETIK
AlphaPeptTools
annbatch
anndata for R
anndataR
annsel
ATLAS
benGRN
bento-tools
biolord
cell2location
Cell_BLAST
CellAnnotator
CellCharter
CellMapper
CellOracle
CellphoneDB
CellRank
cellxgene
Cirrocumulus
clone2vec
dandelion
delnx
DOTools_py
DoubletDetection
DRVI
dvp-io
dynamo-release
epiScanpy
eschr
fava
flashdeconv
flowsom
GPTBioInsightor
grassp
GRnnData
gssnng
hotspot
illico
infercnvpy
kompot
LazySlide
liana
Marsilea
maxspin
moscot
Mowgli
Multivelo
ncountr
NicheNetPy
nichepca
novae
omicverse
Palantir
Panpipes
ParTIpy
PathML
pcdl
PEAKQC
pegasus
PILOT
popV
pycea
pychromVAR
pyCrossTalkeR
PyDESeq2
pyLemur
pySCENIC
pytximport
pyUCell
Rectangle
SC2Spa
SCALEX
scanpro
scCellFie
scDataLoader
scFates
scGen
schist
scib
scib-metrics
scib-rapids
scmcp
scPRINT
scPRINT-2
scTriangulate
scVelo
scviva-tools
scxmatch
scXpand
scyan
sift-sc
sincei
Sobolev Alignment
sopa
spatial-eggplant
spatialdataR
spatialproteomics
spatiomic
STMiner
Symphonypy
tangram
TAU Community Detection
TreeData
vitessce
wsidata
zellkonverter
scanpy.pl.StackedViolin.DEFAULT_DENSITY_NORM
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